The Python Macromolecular Library (mmLib) is a software toolkit and library of routines for the analysis and manipulation of macromolecular structural models, implemented in the Python programming language. It is accessed via a layered, object-oriented application programming interface, and provides a range of useful software components for parsing mmCIF, PDB, and MTZ files, a library of atomic elements and monomers, an object-oriented data structure describing biological macromolecules, and an OpenGL molecular viewer.

This package runs remote analyses on a Pise Web server. There are currently about 300 programs available, including EMBOSS and Phylip, several phylogeny, sequence comparison, 3D structure, pattern discovery, gene prediction and DNA, protein or RNA analyses programs. The package automatically chain programs to extract results as file, string or filehandle for Biopython modules. It also accepts Biopython sequences and alignment class as input data.

OIO is a free (as in GPL) web-based research and clinical data system that provides user-extensible plug-and-play components and data mining tools. We use it at Harbor-UCLA for health/treatment outcomes data. Forms/metadata can be exported+imported as XML and exchanged via the online OIO Library at www.TxOutcome.Org. It is written in Zope/Python and uses the PostgreSQL database backend. It has not been used to manage gene sequence/annotation data to my knowledge but it would be trivial to extend it for those functions.

PyPhy is a set of python scripts and modules for automatic, large-scale reconstructions of phylogenetic relationships of complete microbial genomes. PyPhy consists of AutoTree which automatically generates phylogenetic trees for each amino acid sequence in a FASTA file, and Xphylome which generates and visualizes the Phylome Maps for a microbial genome.

This site contains code dealing with structural bioinformatics and molecular visualization. This includes MolKit, which reads molecules from a number of file formats; PyBabel, which builds up molecular structures; MSLib, which wraps up a molecular surface calculation library; Python Molecular Viewer (PMV), which provides a complete viewer; AutoDockTools, which provides a GUI to set up ligand to protein docking experiments; and many more.

Contains the Molecular Modeling Toolkit (MMTK), an open source program library for molecular simulation applications. Additionally, Konrad has ScientificPython, which collects a number of modules that are useful in scientific computing, including code for statistics, basic geometry, etc.

This collects Paul's modules for doing different tasks (and also has links and a nice essay about why he likes python). A particularly interesting module is disipyl, which provides an object oriented interface to the Dislin plotting library.

A collection of python modules and scripts originally intended to process large collections of HIV sequences. Now contains general utilities for sequence analysis, manipulation, classification, and formatting. Plus other useful stuff.

This is a package for RNA secondary structure prediction and comparison. While it was not specifically written for Python, you can get the Python wrappers for it using the SWIG file that is included with the software package. The easiest way is to first compile the Vienna RNA package as described in its documentation (you don't need to actually install it). Then, run "swig -python RNA.i" in the ViennaRNA-1.8.4/Perl directory. This will create a new RNA_wrap.c specifically for Python, as well as RNA.py.

Next, you should compile RNA_wrap.c. You can use this setup.py script: